Sigh. I never knew about the object subfolders. Maybe the fact that they don't appear in dialogues threw me off, but either way I'm glad to see that's already partially there and the rest is slowly but surely in the works.
As for how variable folders would work... I cobbled together some mock-ups to show what I mean, since the following text description by itself is very much inadequate.
You can add folders using a new button on top of the "Edit variables" list, and then add another attribute to variables underneath "Initial value" and "Description", for "Folder". Maybe make an easier way to add multiple variables to the same folder by highlighting all of them, rightclicking, and selecting "Add all to folder".
It's not as ideal as drag and dropping, but it's definitely doable. You'd have to change several things here and there, of course, and for all I know it's far more complicated than it looks, but I would heavily abuse this feature if it were ever put in. Jus' saying.